SMTL ID : 6o3u.3 (3 other biounits)

Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1.H4K3 in complex with 06:0 PA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: P.60, G.61, R.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.61, A:R.62 GOL.2: 2 residues within 4Å: Chain B: R.63, R.67 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.63, B:R.63, B:R.67

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain B: K.12, S.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.16, B:S.16 Salt bridges: B:K.12 SO4.4: 2 residues within 4Å: Chain B: Q.43, R.44 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.44 Salt bridges: B:R.44 SO4.5: 10 residues within 4Å: Chain A: S.163, S.177, T.179 Chain B: F.177, P.178, A.179, V.180, S.188, L.189, S.190 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.163, A:S.163, A:S.177, A:T.179, B:V.180

2 x 44E: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate(Non-covalent)

44E.6: 4 residues within 4Å: Chain B: S.28, F.29, S.30, S.31 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.29, B:S.30, B:S.31 44E.7: 4 residues within 4Å: Chain B: A.72, D.73, R.74, S.75 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.72, B:D.73, B:R.74, B:S.75 Salt bridges: B:R.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., An MPER antibody neutralizes HIV-1 using germline features shared among donors. Nat Commun (2019)

Release Date

2019-12-04

Peptides

PGZL1.H4K3 light chain: A
PGZL1.H4K3 heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

PGZL1.H4K3 light chain

PGZL1.H4K3 heavy chain

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